I mean how it emphasizes battle scenes at the expense of everything else.
On one hand, with characters, although a decent standard is met (the two sisters have some good scenes that show off their relationship, and there is even a much welcome, if a bit shallow, scene with Nanoha and Alisa), I would certainly appreciate more time devoted to depicting their personalities and relationships. The amusement park provided an excellent chance to show them just having fun. I'd also have liked more downtime between battles - maybe a bathtime conversation after a defeat where they each try to cope with it?
On the other hand, the plot rushes forward clumsily at times. That scene where the girls are shown a seemingly irrelevant inanimate object just so the viewer will know about it is a tad too obvious. The betrayal
scene, too, could use some more subtlety.
Back to my main point, these are all tradeoffs and choices that I understand made sense for the previous movies, but when planning a multi-movie story that's not an alternate version to an existing anime, I'm a bit disappointed that they went with this particular recipe. The result is good, just not the one I'd have liked best.
As for that thing about the manga, as you can imagine I was taking a blind guess at what the source material was. I could have looked it up, but sometimes I prefer to make my ignorance obvious so others can gauge how much credibility my posts deserve.